All modules for which code is available

• simplicity.dir_manager
• simplicity.evolution.decoder
• simplicity.evolution.mutations
• simplicity.evolution.reference
• simplicity.extrande
• simplicity.intra_host_model
• simplicity.output_manager
• simplicity.phenotype.consensus
• simplicity.phenotype.distance
• simplicity.phenotype.update
• simplicity.phenotype.weight
• simplicity.plots_manager
• simplicity.population
• simplicity.population_model
• simplicity.random_gen
• simplicity.runme
• simplicity.runners
• simplicity.runners.multiprocessing
• simplicity.runners.serial
• simplicity.runners.slurm
• simplicity.runners.unit_run
• simplicity.settings_manager
• simplicity.simulation
• simplicity.tree.json_tree
• simplicity.tree.newick
• simplicity.tree.nexus
• simplicity.tree.tree_builder
• simplicity.tuning.diagnosis_rate
• simplicity.tuning.evolutionary_rate